Actinobacillus actinomycetemcomitans is a Gram-negative bacterium which has an important role in localized juvenile and in progressive periodontitis. It is sensitive to killing by the myeloperoxidase (MP)-hydrogen peroxide (H2O2)-chloride system which is part of the innate host defense mediated by polymorphonuclear leukocytes. Since it has been recently suggested that thiocyanate, instead of chloride, could serve as a main substrate for MP as for lactoperoxidase (LP) and salivary peroxidase, we investigated in this study the effect of both LP and MP systems on A. actinomycetemcomitans with different (pseudo) halide substrates, thiocyanate, chloride and iodide. The concentrations of the substrates were physiological for oral fluids, as was the concentration range of H2O2. Both peroxidases produced end products with identical antibacterial activity with thiocyanate and iodide. The oxidation of iodide resulted in the highest antimicrobial efficiency followed by chloride and thiocyanate. Addition of thiocyanate into either MP-H2O2-chloride or MP/LP-H2O2-iodide system abolished the bactericidal activity of the oxidized halide. However, the chloride did not affect the bactericidality of the MP-H2O2-iodide system, but when all 3 (pseudo) halide substrates were present no antimicrobial effect was recorded. Our study shows that the presence of thiocyanate in physiological amounts is able to prevent the bactericidal activity of halide-peroxidase systems in low H2O2 concentrations. These results explain why thiocyanate-peroxidase systems of either innate origin (saliva, crevicular fluid) or introduced by commercial oral hygiene products are most probably ineffective against A. actinomycetemcomitans in vivo. Further studies of halide/thiocyanate ratio are needed to develop products which are also effective against oral anaerobes.